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pair_beck.cpp
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Sat, Feb 15, 09:19

pair_beck.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Jonathan Zimmerman (Sandia)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "pair_beck.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "math_special.h"
using namespace LAMMPS_NS;
using namespace MathSpecial;
/* ---------------------------------------------------------------------- */
PairBeck::PairBeck(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairBeck::~PairBeck()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(AA);
memory->destroy(BB);
memory->destroy(aa);
memory->destroy(alpha);
memory->destroy(beta);
}
}
/* ---------------------------------------------------------------------- */
void PairBeck::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r5,force_beck,factor_lj;
double r,rinv;
double aaij,alphaij,betaij;
double term1,term1inv,term2,term3,term4,term5,term6;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
r5 = rsq*rsq*r;
aaij = aa[itype][jtype];
alphaij = alpha[itype][jtype];
betaij = beta[itype][jtype];
term1 = aaij*aaij + rsq;
term2 = powint(term1,-5);
term3 = 21.672 + 30.0*aaij*aaij + 6.0*rsq;
term4 = alphaij + r5*betaij;
term5 = alphaij + 6.0*r5*betaij;
rinv = 1.0/r;
force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5;
force_beck -= BB[itype][jtype]*r*term2*term3;
fpair = factor_lj*force_beck*rinv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
term6 = powint(term1,-3);
term1inv = 1.0/term1;
evdwl = AA[itype][jtype]*exp(-1.0*r*term4);
evdwl -= BB[itype][jtype]*term6*(1.0+(2.709+3.0*aaij*aaij)*term1inv);
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairBeck::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(AA,n+1,n+1,"pair:AA");
memory->create(BB,n+1,n+1,"pair:BB");
memory->create(aa,n+1,n+1,"pair:aa");
memory->create(alpha,n+1,n+1,"pair:alpha");
memory->create(beta,n+1,n+1,"pair:beta");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairBeck::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
cut[i][j] = cut_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairBeck::coeff(int narg, char **arg)
{
if (narg != 7 && narg != 8)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double AA_one = force->numeric(FLERR,arg[2]);
double BB_one = force->numeric(FLERR,arg[3]);
double aa_one = force->numeric(FLERR,arg[4]);
double alpha_one = force->numeric(FLERR,arg[5]);
double beta_one = force->numeric(FLERR,arg[6]);
double cut_one = cut_global;
if (narg == 8) cut_one = force->numeric(FLERR,arg[7]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
AA[i][j] = AA_one;
BB[i][j] = BB_one;
aa[i][j] = aa_one;
alpha[i][j] = alpha_one;
beta[i][j] = beta_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairBeck::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
AA[j][i] = AA[i][j];
BB[j][i] = BB[i][j];
aa[j][i] = aa[i][j];
alpha[j][i] = alpha[i][j];
beta[j][i] = beta[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBeck::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&AA[i][j],sizeof(double),1,fp);
fwrite(&BB[i][j],sizeof(double),1,fp);
fwrite(&aa[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&beta[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBeck::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&AA[i][j],sizeof(double),1,fp);
fread(&BB[i][j],sizeof(double),1,fp);
fread(&aa[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&beta[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&AA[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&BB[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&aa[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&beta[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBeck::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBeck::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairBeck::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double phi_beck,r,rinv;
double r5,force_beck;
double aaij,alphaij,betaij;
double term1,term1inv,term2,term3,term4,term5,term6;
r = sqrt(rsq);
r5 = rsq*rsq*r;
aaij = aa[itype][jtype];
alphaij = alpha[itype][jtype];
betaij = beta[itype][jtype];
term1 = aaij*aaij + rsq;
term2 = powint(term1,-5);
term3 = 21.672 + 30.0*aaij*aaij + 6.0*rsq;
term4 = alphaij + r5*betaij;
term5 = alphaij + 6.0*r5*betaij;
rinv = 1.0/r;
force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5;
force_beck -= BB[itype][jtype]*r*term2*term3;
fforce = factor_lj*force_beck*rinv;
term6 = powint(term1,-3);
term1inv = 1.0/term1;
phi_beck = AA[itype][jtype]*exp(-1.0*r*term4);
phi_beck -= BB[itype][jtype]*term6*(1.0+(2.709+3.0*aaij*aaij)*term1inv);
return factor_lj*phi_beck;
}

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